27300d62d155d9941c226a2c27f3a33b3ea53ed0
hiram
  Mon Oct 28 14:15:17 2024 -0700
do not use /dev/shm as a temporary directory refs #34685

diff --git src/hg/utils/automation/asmHubRepeatMasker.sh src/hg/utils/automation/asmHubRepeatMasker.sh
index c061941..92e0225 100755
--- src/hg/utils/automation/asmHubRepeatMasker.sh
+++ src/hg/utils/automation/asmHubRepeatMasker.sh
@@ -7,40 +7,32 @@
 set -beEu -o pipefail
 
 # ensure sort functions properly despite kluster node environment
 export LC_COLLATE=C
 
 if [ $# -ne 3 ]; then
   printf "%s\n" "usage: asmHubRepeatMasker.sh <asmId> <pathTo/*fa.out.gz> <destinationDir/>" 1>&2
   exit 255
 fi
 
 if [ -d "/data/tmp" ]; then
   export TMPDIR="/data/tmp"
 elif [ -d "/scratch/tmp" ]; then
   export TMPDIR="/scratch/tmp"
 else
-  tmpSz=`df --output=avail -k /tmp | tail -1`
-  shmSz=`df --output=avail -k /dev/shm | tail -1`
-  if [ "${shmSz}" -gt "${tmpSz}" ]; then
-     mkdir -p /dev/shm/tmp
-     chmod 777 /dev/shm/tmp
-     export TMPDIR="/dev/shm/tmp"
-  else
   export TMPDIR="/tmp"
 fi
-fi
 export dateStamp=`date "+%FT%T %s"`
 
 export asmId=$1
 export rmOutFile=$2
 export destDir=$3
 export chrSizes=""
 
 if [ -s "$destDir/$asmId.chrom.sizes" ]; then
   chrSizes="$destDir/$asmId.chrom.sizes"
 elif [ -s "../../$asmId.chrom.sizes" ]; then
   chrSizes="../../$asmId.chrom.sizes"
 fi
 
 # assume this file name pattern
 export faAlign=`echo "${rmOutFile}" | sed -e 's/sorted.fa.out/fa.align/; s/.gz//;'`